I'm actually not familiar with this area at all, but I guess the argument is that the smaller screen size of Surface pro 1 and 2 made it different enough from the Wacom tablets, where as Surface Pro 3 kind of fudges that line.
Again, just repeating what I read on another site. I'm not actually familiar with Wacom devices.
Maybe the reason to go with N-Trig was to cut down on cost and they found a way to get rid of the parallax issue (The lag between the pen scroll and the actual output)?
No matter what pen tech is being used, there are going to be compromises. I calibrated my Surface's Wacom pen with over 100 points (as opposed to the default 4), and you still get really weird detection points at the edges.
And because there's sensitivity issues with the angle you're holding a Wacom pen, the pointer isn't always where the pen tip is. This is especially problematic if you like switching between portrait and landscape mode.
Wacom may be the standard, but it's far from perfect.